Cyanobacterial blooms are found in many freshwater ecosystems around the world, but the effect of environmental factors on their growth and the proportion of species still require more investigation. In this study, the physiological responses of bloom-forming cyanobacteria Microcystis aeruginosa FACHB912, Microcystis flos-aquae FACHB1028 and Pseudanabaena sp. FACHB1282 to iron deficiency were investigated. Their specific growth rates were found to decrease as the available iron concentration decreased. At low available iron concentrations of 1 × 10 −7 M (pFe 21.3) and 5 × 10 −8 M (pFe 21.6), M. aeruginosa had the lowest specific growth rate among three studied species. The cell sizes of M. flos-aquae and Pseudanabaena sp. were significantly smaller under the lowest iron concentration. The chlorophyll a content of the three species decreased at the lowest iron concentration. The maximal relative electron transport rate, photosynthetic efficiency, and light-saturation parameter of M. aeruginosa were lower than the other two cyanobacteria at pFe 21.3. Therefore, M. aeruginosa was the least able to adapt to iron deficiency. Under iron deficiency, the functional absorption cross-section of PSII and electron transport rate on the acceptor side of PSII decreased in M. aeruginosa, while the connectivity factor between individual photosynthetic units increased in M. flos-aquae, and the electron transport rate on the acceptor side of PSII and between PSII and PSI decreased in Pseudanabaena sp. The ability to store iron was highest in M. flosaquae, followed by Pseudanabaena sp. and M. aeruginosa. Thus, these results provide necessary information for detecting the role of iron in the succession of cyanobacterial species in Lake Taihu, the third largest freshwater lake in China, because all three species were isolated from this lake. Specific growth rate (%) M. aeruginosa M. flos-aquae Pseudanabaena sp.Fig. 4. The growth curves (a) and specific growth rates (b) of M. aeruginosa, M. flos-aquae and Pseudanabaena sp. at pFe 22.3 (n = 4). The three species were transferred from pFe 20.6 (first transfer), then transferred at the fourth day to fresh medium containing pFe 22.3, and repeated this manipulation every 4 days. The initial values of specific growth rate for M. aeruginosa, M. flos-aquae and Pseudanabaena sp. were 0.420 AE 0.012, 0.272 AE 0.027 and 0.595 AE 0.006. The asterisk on error bars represents significant differences from the other two species under the same transfer (Tukey's HSD, P < 0.05). See the caption in Fig. 1 for other information.